A repository for hosting Nextflow [`DSL2`](https://www.nextflow.io/docs/latest/dsl2.html) module files containing tool-specific process definitions and their associated documentation.
The module files hosted in this repository define a set of processes for software tools such as `fastqc`, `bwa`, `samtools` etc. This allows you to share and add common functionality across multiple pipelines in a modular fashion.
We have written a helper command in the `nf-core/tools` package that uses the GitHub API to obtain the relevant information for the module files present in the `software/` directory of this repository. This includes using `git` commit hashes to track changes for reproducibility purposes, and to download and install all of the relevant module files.
- ~~it MUST be possible to pass additional parameters to the tool as a command line string via the `params.<MODULE>_args` parameter.~~
- it MUST be possible to pass additional parameters as a [nextflow Map](https://www.nextflow.io/docs/latest/script.html#maps) through an additional input channel `val(options)` [Details require discussion].
- All NGS modules MUST accept a triplet [name, single_end, reads] as input. The single-end boolean values MUST be specified through the input channel and not inferred from the data e.g. [here](https://github.com/nf-core/tools/blob/028a9b3f9d1ad044e879a1de13d3c3a25a06b9a7/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/modules/nf-core/fastqc.nf#L13).
- Software that can be piped together SHOULD be added to separate module files unless there is an run-time, storage advantage in implementing in this way e.g. `bwa mem | samtools view -C -T ref.fasta` to output CRAM instead of SAM.
- Each module MUST define a label `process_low`, `process_medium` or `process_high` to declare resource requirements. (*These flags will be ignored outside of nf-core and the pipeline developer is free to define adequate resource requirements*)
- The module MUST accept the parameters `params.out_dir` and `params.publish_dir` and MUST publish results into `${params.out_dir}/${params.publish_dir}`.
- Every module MUST be tested by adding a test workflow with a toy dataset.
- Test data MUST be stored within this repo. It is RECOMMENDED to re-use generic files from `tests/data` by symlinking them into the test directory of the module. Specific files MUST be added to the test-directory directly. Test files MUST be kept as tiny as possible.
- Software requirements SHOULD be declared in a conda `environment.yml` file, including exact version numbers. Additionally, there MUST be a `Dockerfile` that containerizes the environment, or packages the software if conda is not available.
- Docker containers MUST BE identified by their `sha256(Dockerfile + environment.yml)`.
- Each module must have it's own `Dockerfile` and `environment.yml` file
- Care should be taken to maintain identical files for subcommands that use the same software. Then the hash tag will be the same and they will be implicitly re-used across subcommands.
- A module MUST be documented in the `meta.yml` file. It MUST document `params`, `input` and `output`. `input` and `output` MUST be a nested list. [Exact detail need to be elaborated. ]
[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/modules` repository to your own GitHub account. Within the local clone of your fork add the module file to the [`nf-core/modules/software`](https://github.com/nf-core/modules/tree/master/software) directory. Please keep the naming consistent between the module and documentation files e.g. `bwa.nf` and `bwa.md`, respectively.
Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on `nf-core/modules` GitHub repo with the appropriate information.
We will be notified automatically when you have created your pull request, and providing that everything adheres to nf-core guidelines we will endeavour to approve your pull request as soon as possible.
The features offered by Nextflow DSL2 can be used in various ways depending on the granularity with which you would like to write pipelines. Please see the listing below for the hierarchy and associated terminology we have decided to use when referring to DSL2 components:
- *Module*: A `process` that can be used within different pipelines and is as atomic as possible i.e. cannot be split into another module. An example of this would be a module file containing the process definition for a single tool such as `FastQC`. At present, this repository has been created to only host atomic module files that should be added to the `software/` directory along with the required documentation and tests.
- *Sub-workflow*: A chain of multiple modules that offer a higher-level of functionality within the context of a pipeline. For example, a sub-workflow to run multiple QC tools with FastQ files as input. Sub-workflows should be shipped with the pipeline implementation and if required they should be shared amongst different pipelines directly from there. As it stands, this repository will not host sub-workflows although this may change in the future since well-written sub-workflows will be the most powerful aspect of DSL2.
- *Workflow*: What DSL1 users would consider an end-to-end pipeline. For example, from one or more inputs to a series of outputs. This can either be implemented using a large monolithic script as with DSL1, or by using a combination of DSL2 individual modules and sub-workflows.
For further information or help, don't hesitate to get in touch on [Slack `#modules` channel](https://nfcore.slack.com/channels/modules) (you can join with [this invite](https://nf-co.re/join/slack)).
If you use the module files in this repository for your analysis please you can cite the `nf-core` publication as follows:
> **The nf-core framework for community-curated bioinformatics pipelines.**
>
> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
>
> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
The module files hosted in this repository define a set of processes for software tools such as `fastqc`, `trimgalore`, `bwa` etc. This allows you to share and add common functionality across multiple pipelines in a modular fashion.
> The definition and standards for module files are still under discussion amongst the community but hopefully, a description should be added here soon!
### Offline usage
If you want to use an existing module file available in `nf-core/modules`, and you're running on a system that has no internet connection, you'll need to download the repository (e.g. `git clone https://github.com/nf-core/modules.git`) and place it in a location that is visible to the file system on which you are running the pipeline. Then run the pipeline by creating a custom config file called e.g. `custom_module.conf` containing the following information:
```bash
include /path/to/downloaded/modules/directory/
```
Then you can run the pipeline by directly passing the additional config file with the `-c` parameter:
```bash
nextflow run /path/to/pipeline/ -c /path/to/custom_module.conf
```
> Note that the nf-core/tools helper package has a `download` command to download all required pipeline
> files + singularity containers + institutional configs + modules in one go for you, to make this process easier.
